Package | Description |
---|---|
com.compomics.util.experiment |
Gene factory classes.
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
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com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.io.identifications |
Experiment identification classes.
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com.compomics.util.experiment.io.identifications.idfilereaders |
Experiment classes related to reading search engine files.
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com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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com.compomics.util.preferences |
Utilities preferences classes.
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com.compomics.util.pride |
Objects related to mapping to PRIDE.
|
Modifier and Type | Method and Description |
---|---|
static ShotgunProtocol |
ShotgunProtocol.inferProtocolFromSearchSettings(SearchParameters searchParameters)
Backward compatibility inferring the protocol from search settings.
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Modifier and Type | Method and Description |
---|---|
ArrayList<String> |
PTMFactory.loadBackedUpModifications(SearchParameters searchParameters,
boolean overwrite)
Verifies that the modifications backed-up in the search parameters are
loaded and alerts the user in case conflicts are found.
|
Modifier and Type | Method and Description |
---|---|
void |
PeptideAssumptionFilter.setFilterFromSearchParameters(SearchParameters searchParameters)
Updates the filter based on the search parameters.
|
boolean |
PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption,
String spectrumKey,
SpectrumFactory spectrumFactory,
SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchParameters.getIdentificationParameters(File searchParametersFile)
Loads the identification parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SearchParameters.equals(SearchParameters otherSearchParameters)
Returns true if the search parameter objects have identical settings.
|
static void |
SearchParameters.saveIdentificationParameters(SearchParameters searchParameters,
File searchParametersFile)
Saves the identification parameters to a serialized file.
|
void |
SearchParameters.setDefaultAdvancedSettings(SearchParameters searchParameters)
Set the advanced settings to the values in the given search parameters
object or to the default values of the advanced settings are not set for
a given advocate.
|
Constructor and Description |
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SearchParameters(SearchParameters searchParameters)
Constructor.
|
Constructor and Description |
---|
FMIndex(WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsPreferences peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress,
int nThreads)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationSettings.setPreferencesFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on search parameters.
|
Constructor and Description |
---|
AnnotationSettings(SearchParameters searchParameters)
Constructor setting preferences from search parameters.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
static String |
MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
Modifier and Type | Method and Description |
---|---|
SearchParameters |
SearchSettingsDialog.getSearchParameters()
Returns a SearchParameters instance based on the user input in the GUI.
|
Constructor and Description |
---|
GenePreferencesDialog(JDialog owner,
Frame parentFrame,
GenePreferences genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a dialog as owner.
|
GenePreferencesDialog(JFrame parentFrame,
GenePreferences genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a frame as owner.
|
SearchSettingsDialog(Dialog owner,
Frame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
ConfigurationFile configurationFile,
LastSelectedFolder lastSelectedFolder,
String settingsName,
boolean editable)
Creates a new SearchSettingsDialog with a dialog as owner.
|
SearchSettingsDialog(Frame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
ConfigurationFile configurationFile,
LastSelectedFolder lastSelectedFolder,
String settingsName,
boolean editable)
Creates a new SearchSettingsDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
IdentificationParameters.getSearchParameters()
Returns the parameters used for the spectrum matching.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParameters.setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
|
void |
GenePreferences.setPreferencesFromSearchParameters(SearchParameters searchParameters)
Sets the preferences from the given search parameters.
|
void |
IdentificationParameters.setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
|
Constructor and Description |
---|
IdentificationParameters(SearchParameters searchParameters)
Creates default identification parameters from the given search
parameters.
|
IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationSettings annotationSettings,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideVariantsPreferences peptideVariantsPreferences,
GenePreferences genePreferences,
PsmScoringPreferences psmScoringPreferences,
PeptideAssumptionFilter peptideAssumptionFilter,
PTMScoringPreferences ptmScoringPreferences,
ProteinInferencePreferences proteinInferencePreferences,
IdMatchValidationPreferences idValidationPreferences,
FractionSettings fractionSettings)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
static PtmToPrideMap |
PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)
Deprecated.
the CV term is now part of the PTM object
|
Copyright © 2018. All rights reserved.